The Albert Einstein hospital in Sao Paulo says the 74-year-old Pele is "clinically stable" and "recovering" from today's procedure.
Pele was hospitalised yesterday evening after cancelling his appearance at an event at the Pele Museum in the coastal city of Santos because of stomach pain.
Doctors said in the hospital's statement that tests conducted after Pele was admitted showed that the kidney stones were "obstructing" his urinary tract.
The hospital did not say when Pele was expected to be released.